BatchJobs v1.8
0
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Batch Computing with R
Provides Map, Reduce and Filter variants to generate jobs on batch
computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine.
Multicore and SSH systems are also supported. For further details see the
project web page.
Functions in BatchJobs
| Name | Description | |
| batchExpandGrid | Map function over all combinations. | |
| cfReadBrewTemplate | Cluster functions helper: Read in your brew template file. | |
| callFunctionOnSSHWorkers | Call an arbitrary function on specified SSH workers. | |
| makeClusterFunctionsSSH | Create an SSH cluster to execute jobs. | |
| getResources | Function to get job resources in job function. | |
| makeRegistry | Construct a registry object. | |
| makeJob | Creates a job description. | |
| getSSHWorkersInfo | Print and return R installation and other information for SSH workers. | |
| showLog | Display the contents of a log file. | |
| makeClusterFunctionsTorque | Create cluster functions for torque-based systems. | |
| cfBrewTemplate | Cluster functions helper: Brew your template into a job description file. | |
| debugMulticore | Helper function to debug multicore mode. | |
| showStatus | Retrieve or show status information about jobs. | |
| addRegistrySourceDirs | Add source dirs to registry. | |
| cfHandleUnknownSubmitError | Cluster functions helper: Handle an unknown error during job submission. | |
| sweepRegistry | Sweep obsolete files from the file system. | |
| filterResults | Find all results where a specific condition is true. | |
| batchQuery | Manually query the BatchJobs database | |
| batchReduce | Reduces via a binary function over a list adding jobs to a registry. | |
| addRegistrySourceFiles | Add source files to registry. | |
| findJobs | Finds ids of jobs that match a query. | |
| debugSSH | Helper function to debug SSH mode. | |
| cfKillBatchJob | Cluster functions helper: Kill a batch job via OS command | |
| batchUnexport | Unload exported R objects. | |
| findDone | Find jobs depending on computional state. | |
| getErrorMessages | Get error messages of jobs. | |
| checkIds | Check job ids. | |
| configuration | BatchJobs configuration. | |
| getConfig | Returns a list of BatchJobs configuration settings | |
| syncRegistry | Syncronize staged queries into the registry. | |
| getJobLocation | Get the physical location of job files on the hard disk. | |
| copyRequiredJobFiles | ONLY FOR INTERNAL USAGE. | |
| getJobIds | Get ids of jobs in registry. | |
| getJobParamDf | Retrieve Job Parameters. | |
| getJobNr | Get number of jobs in registry. | |
| getJobInfo | Get computational information of jobs. | |
| makeClusterFunctionsSLURM | Create cluster functions for SLURM-based systems. | |
| makeClusterFunctionsSGE | Create cluster functions for Sun Grid Engine systems. | |
| reduceResults | Reduce results from result directory. | |
| getJobResources | Function to get the resources that were submitted for some jobs. | |
| removeRegistry | Remove a registry object. | |
| loadExports | Load exported R data objects. | |
| sanitizePath | Sanitize a path | |
| killJobs | Kill some jobs on the batch system. | |
| loadConfig | Load a specific configuration file. | |
| getJobs | Get jobs from registry by id. | |
| getLogFiles | Get log file paths for jobs. | |
| dbGetJobs | ONLY FOR INTERNAL USAGE. | |
| dbCreateJobDefTable | ONLY FOR INTERNAL USAGE. | |
| loadRegistry | Load a previously saved registry. | |
| removeRegistrySourceFiles | Remove source files from registry. | |
| loadResult | Loads a specific result file. | |
| setRegistryPackages | Set packages for a registry. | |
| resetJobs | Reset computational state of jobs. | |
| showClusterStatus | Show information about available computational resources on cluster. | |
| makeClusterFunctionsLSF | Create cluster functions for LSF systems. | |
| testJob | Tests a job by running it with Rscript in a new process. | |
| loadResults | Loads result files for id vector. | |
| makeClusterFunctions | Create a ClusterFuntions object. | |
| setConfig | Set and overwrite configuration settings | |
| makeClusterFunctionsLocal | Create cluster functions for sequential execution on local host. | |
| setJobFunction | Sets the job function for already existing jobs. | |
| updateRegistry | ONLY FOR INTERNAL USAGE. | |
| waitForJobs | Wait for termination of jobs on the batch system. | |
| setJobNames | Set job names. | |
| getJob | Get job from registry by id. | |
| makeClusterFunctionsInteractive | Create cluster functions for sequential execution in same session. | |
| grepLogs | Grep log files for a pattern. | |
| installPackagesOnSSHWorkers | Install packages on SSH workers. | |
| removeRegistryPackages | Remove packages from registry. | |
| makeClusterFunctionsMulticore | Use multiple cores on local Linux machine to spawn parallel jobs. | |
| removeRegistrySourceDirs | Remove packages from registry. | |
| makeClusterFunctionsOpenLava | Create cluster functions for OpenLava systems. | |
| makeSSHWorker | Create SSH worker for SSH cluster functions. | |
| makeSubmitJobResult | Create a SubmitJobResult object. | |
| submitJobs | Submit jobs or chunks of jobs to batch system via cluster function. | |
| sourceRegistryFiles | Source registry files | |
| batchMapResults | Maps a function over the results of a registry by using batchMap. | |
| batchExport | Export R object to be available on the slaves. | |
| BatchJobs | The BatchJobs package | |
| batchMap | Maps a function over lists or vectors, adding jobs to a registry. | |
| batchMapQuick | Combination of makeRegistry, batchMap and submitJobs. | |
| addRegistryPackages | Add packages to registry. | |
| applyJobFunction | applyJobFunction ONLY FOR INTERNAL USAGE. | |
| batchReduceResults | Reduces results via a binary function and adds jobs for this to a registry. | |
| No Results! | ||
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Details
| URL | https://github.com/tudo-r/BatchJobs |
| BugReports | https://github.com/tudo-r/BatchJobs/issues |
| MailingList | batchjobs@googlegroups.com |
| License | BSD_2_clause + file LICENSE |
| LazyData | yes |
| ByteCompile | yes |
| RoxygenNote | 6.1.1 |
| Encoding | UTF-8 |
| NeedsCompilation | no |
| Packaged | 2019-05-09 08:41:04 UTC; lang |
| Repository | CRAN |
| Date/Publication | 2019-05-14 22:00:16 UTC |
| imports | backports (>= 1.1.1) , brew , checkmate (>= 1.8.0) , data.table (>= 1.9.6) , DBI , digest , parallel , RSQLite (>= 1.0.9011) , sendmailR , stats , stringi (>= 0.4-1) , utils |
| depends | BBmisc (>= 1.9) , methods , R (>= 3.0.0) |
| suggests | MASS , testthat |
| Contributors | Michel Lang, Bernd Bischl, Henrik Bengtsson |
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